Co-reporter:Dongbo Zhao, Ling Yang, Yigao Yuan, Hanchen Wang, Hao Dong, and Shuhua Li
The Journal of Physical Chemistry B November 2, 2017 Volume 121(Issue 43) pp:10064-10064
Publication Date(Web):October 11, 2017
DOI:10.1021/acs.jpcb.7b09067
Foldamer, inspired by the structures and functions of biopolymers, is defined as an artificial molecular architecture that can fold into a three-dimensional structure in solution and has been a growing and active field in supramolecular chemistry. The central issue in foldamer science is to understand how the primary sequence of oligomer folds into conformationally ordered structures as well as how individual subunits self-associate into assembly. For duplex structures, these two issues are always interrelated and inseparable with each other. Although the emergence of new foldamer keeps growing, the detailed mechanism remains elusive. On the basis of an artificially synthesized arylamide oligoamide foldamer with its crystal structure available, we constructed a set of four foldamers with a similar backbone but different substituents and aimed at dissecting the folding and self-association mechanisms of a double-helical foldamer with computations. Using molecular simulations at a microsecond time scale, we observed very consistent processes of the spontaneous self-assembly of two single-helical motifs into an entwined complex. Our results reveal that aggregation of two single-helical motifs driven by extensive π–π interactions is energetically favorable and that this spontaneous self-assembly proceeds through an “unwinding–threading–rewinding” mechanism. The detailed mechanisms about the folding and self-assembly in an aromatic oligoamide foldamer we present here disclose how the sequence is associated with a well-ordered three-dimensional structure at atomic level and therefore may have implications for designing new foldamers with versatile functions.
Co-reporter:Dongbo Zhao, Ruiheng Song, Wei Li, Jing Ma, Hao Dong, and Shuhua Li
Journal of Chemical Theory and Computation November 14, 2017 Volume 13(Issue 11) pp:5231-5231
Publication Date(Web):October 4, 2017
DOI:10.1021/acs.jctc.7b00380
The generalized energy-based fragmentation (GEBF) method is extended to allow calculations of nuclear magnetic resonance (NMR) chemical shifts of macromolecular and condensed-phase systems feasible at a low computational cost. In this approach, NMR shielding constants in a large system are evaluated as a linear combination of the corresponding quantities from a series of small “electrostatically embedded” subsystems. Comparison of NMR shielding constants from the GEBF-X method [where X is an electronic structure method, such as Hartree–Fock (HF), density functional theory (DFT), ...] with those from the conventional quantum chemistry method for two representative systems verifies that the GEBF approach can reproduce the results of the conventional quantum chemistry method very well. This procedure has further been applied to compute NMR shielding constants of a large foldamer and a supramolecular aggregate, and the 15N shielding constant for CH3CN in the CHCl3 solvent. For the former two systems, the predicted 1H chemical shifts are in good agreement with the experimental data. For the CH3CN/CHCl3 solution, the 15N shielding constant of CH3CN is evaluated as the ensemble average of up to 200 sufficiently large CH3CN/CHCl3 clusters from either classical or QM/MM (quantum mechanics/molecular mechanics) molecular dynamics (MD) simulations. Our results reveal that the gas-to-solution shift of 15N (from an isolated CH3CN to the CH3CN/CHCl3 solution) based on PM6-DH+/MM MD simulation is in good accord with the experimental value, outperforming those based on classical MD simulation and the previous polarizable continuum model using integral equation formalism (IEF-PCM) study. This study unravels that the generation of representative liquid structures is critical in evaluating the NMR shielding constants of condensed-phase systems.
The Journal of Organic Chemistry March 17, 2017 Volume 82(Issue 6) pp:2984-2984
Publication Date(Web):February 22, 2017
DOI:10.1021/acs.joc.6b03050
The reaction mechanism of the C–H bond activation of toluene promoted by the hypervalent iodine compound TIPP-I(OH)OTs was investigated in detail by density functional theory calculations. Our calculations show that a plausible reaction pathway of the C–H bond activation of toluene contains two stages: (1) the ligand exchange process on TIPP-I(OH)OTs, involving the substitution of the hydroxyl group and tosyloxyl group with TfOH, and (2) the C–H bond activation of toluene promoted by the hypervalent iodine center with the assistance of the triflate anion. The second step is the rate-limiting step with a relatively low free energy barrier of 19.6 kcal mol–1 in acetonitrile, which is in accord with the experimental fact that the reaction takes place at room temperature. Frontier molecular orbits and natural population analysis show that partial electron transfer from the toluene to the hypervalent iodine moiety occurs in the charge-transfer complex, resulting in the activation of the C–H bond at the para position of toluene. Further calculations show that this hypervalent iodine compound promoted C–H bond activation reaction will be effective if the substrate is electron-rich and a strong Brønsted acid is used.
Co-reporter:Guoqiang Wang, Jia Cao, Liuzhou Gao, Wenxin Chen, Wenhao Huang, Xu Cheng, and Shuhua Li
Journal of the American Chemical Society March 15, 2017 Volume 139(Issue 10) pp:3904-3904
Publication Date(Web):February 17, 2017
DOI:10.1021/jacs.7b00823
Density functional theory investigations revealed that the pyridine-boryl radical generated in situ using 4-cyanopyridine and bis(pinacolato)diboron could be used as a bifunctional “reagent”, which serves as not only a pyridine precursor but also a boryl radical. With the unique reactivity of such radicals, 4-substituted pyridine derivatives could be synthesized using α,β-unsaturated ketones and 4-cyanopyridine via a novel radical addition/C—C coupling mechanism. Several controlled experiments were conducted to provide supportive evidence for the proposed mechanism. In addition to enones, the scope could be extended to a wide range of boryl radical acceptors, including various aldehydes and ketones, aryl imines and alkynones. Lastly, this transformation was applied in the late-stage modification of a complicated pharmaceutical molecule.
Co-reporter:Dandan Yuan, Yunzhi Li, Zhigang Ni, Peter Pulay, Wei Li, and Shuhua Li
Journal of Chemical Theory and Computation June 13, 2017 Volume 13(Issue 6) pp:2696-2696
Publication Date(Web):May 7, 2017
DOI:10.1021/acs.jctc.7b00284
The generalized energy-based fragmentation (GEBF) method has been applied to investigate relative energies of large water clusters (H2O)n (n = 32, 64) with the coupled-cluster singles and doubles with noniterative triple excitations (CCSD(T)) and second-order Møller–Plesset perturbation theory (MP2) at the complete basis set (CBS) limit. Here large water clusters are chosen to be representative structures sampled from molecular dynamics (MD) simulations of liquid water. Our calculations show that the GEBF method is capable of providing highly accurate relative energies for these water clusters in a cost-effective way. We demonstrate that the relative energies from GEBF-MP2/CBS are in excellent agreement with those from GEBF-CCSD(T)/CBS for these water clusters. With the GEBF-CCSD(T)/CBS relative energies as the benchmark results, we have assessed the performance of several theoretical methods widely used for ab initio MD simulations of liquids and aqueous solutions. These methods include density functional theory (DFT) with a number of different functionals, MP2, and density functional tight-binding (the third generation, DFTB3 in short). We find that MP2/aug-cc-pVDZ and several DFT methods (such as LC-ωPBE-D3 and ωB97XD) with the aug-cc-pVTZ basis set can provide satisfactory descriptions for these water clusters. Some widely used functionals (such as B3LYP, PBE0) and DFTB3 are not accurate enough for describing the relative energies of large water clusters. Although the basis set dependence of DFT is less than that of ab initio electron correlation methods, we recommend the combination of a few best functionals and large basis sets (at least aug-cc-pVTZ) in theoretical studies on water clusters or aqueous solutions.
Chemical Science (2010-Present) 2017 vol. 8(Issue 2) pp:1303-1308
Publication Date(Web):2017/01/30
DOI:10.1039/C6SC03888C
A novel and straightforward strategy for functionalized 1H-indazoles is realized by the Rh(III)-catalyzed double C–H activation and C–H/C–H cross coupling of readily available aldehyde phenylhydrazones. The reaction is scalable and various 1H-indazoles could be afforded in moderate to high yields with good functional-group compatibility. Mechanism experiments and DFT calculations suggest the distinctive Rh(III)-catalyzed C–H/C–H cross coupling reaction underwent a cascade C(aryl)–H bond metalation, C(aldhyde)–H bond insertion and reductive elimination process.
Co-reporter:Yunzhi Li;Guoqiang Wang;Wei Li;Yue Wang
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 27) pp:17516-17520
Publication Date(Web):2017/07/12
DOI:10.1039/C7CP03584E
A refined QM/MM approach demonstrated that a monomer model is suitable for describing the emission spectra of crystals without the π⋯π stacking interaction. Whereas for the crystals with notable intermolecular π⋯π stacking interaction, the most stable trimer model (or at least a dimer model) should be used for accurately describing the corresponding emission spectra. This approach is applied to understand the emission properties of two kinds of organic polymorphs.
Three kinds of chiral BINOL-based polymers could be synthesized by polymerization in a Pd-catalyzed cross-coupling reaction. The resulting chiral polymers can exhibit strong mirror image Cotton effects. Interestingly, only P2 and P3 can emit circularly polarized luminescence (CPL) signals, which can be attributed to the chirality transfer of the BINOL moiety via the rigid π-conjugation chain backbone structure system. This work can develop a new strategy for the design of novel CPL materials.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2017 Volume 179(Volume 179) pp:
Publication Date(Web):15 May 2017
DOI:10.1016/j.saa.2017.02.037
•PBC-GEBF method developed by us is first time employed to calculate the vibrational spectra of the DNA nucleobase crystals.•Normal modes are obtained to illustrate the vibrational modes.•Some absorption peaks of crystals were first reported here in the vicinity of 0.5–9 THz.•All the vibrational modes of DNA nucleobase crystals belong to collective vibrational modes in THz range.Terahertz (THz) spectra of DNA nucleobase crystals were experimentally studied by terahertz time domain spectroscopy (THz-TDS), Fourier transform infrared spectroscopy (FTIR), and computationally studied by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). We analyzed the vibrational spectra of solid-state DNA nucleobases and assigned the corresponding vibrational modes to the main peaks in the experimental spectra with the PBC-GEBF results. The computational results were verified to be in good accordance with the experimental data. Harmonic vibrational frequency results revealed that all the vibrational modes belong to collective vibrational modes, which involve complicated mixtures of inter- and intramolecular displacements, somewhere in the vicinity of 0.5–9 THz.From the crystal structure to the vibration spectrum and the corresponding vibration modes.Download high-res image (128KB)Download full-size image
Density functional theory calculations were performed to elucidate the mechanism of the methylation reaction of the N,N-dimethylaminopyridine (DMAP)-modified meta-phenylene ethynylene foldamer with eight methyl sulfonate esters with different alkyl groups. The helical structure of the DMAP-modified mPE foldamer results from multiple intramolecular π–π stacking interactions between m-phenylene ethynylene arms, which can be characterized by the helical energy. The noncovalent interactions between the foldamer and the substrate can stabilize the transition state and result in an acceleration of the methylation reaction of the foldamer. Due to the different shapes of the alkyl chains of the methylating agents, the methylation rates of the foldamers with linear and branched substrates show different rules. It is expected that these mechanistic insights into supramolecular catalysis can be used in the design and preparation of supramolecular catalysts and reactors.
Co-reporter:Manyi Yang, Jingxiang Zou, Guoqiang Wang, and Shuhua Li
The Journal of Physical Chemistry A 2017 Volume 121(Issue 6) pp:
Publication Date(Web):January 27, 2017
DOI:10.1021/acs.jpca.6b12195
We proposed and implemented a combined molecular dynamics and coordinate driving (MD/CD) method for automatically searching multistep reaction pathways of chemical reactions. In this approach, the molecular dynamic (MD) method at the molecular mechanics (MM) or semiempirical quantum mechanical (QM) level is employed to explore the conformational space of the minimum structures, and the modified coordinate driving (CD) method is used to build reaction pathways for representative conformers. The MD/CD method is first applied to two model reactions (the Claisen rearrangement and the intermolecular aldol reaction). By comparing the obtained results with those of the existing methods, we found that the MD/CD method has a comparable performance in searching low-energy reaction pathways. Then, the MD/CD method is further applied to investigate two reactions: the electrocyclic reaction of benzocyclobutene-7-carboxaldehyde and the intramolecular Diels–Alder reaction of ketothioester with 11 effectively rotatable single bonds. For the first reaction, our results can correctly account for its torquoselectivity. For the second one, our method predicts eight reaction channels, leading to eight different stereo- and regioselective products. The MD/CD method is expected to become an efficient and cost-effective theoretical tool for automatically searching low-energy reaction pathways for relatively complex chemical reactions.
Co-reporter:Mingxing Zhang, Bin Li, Yunzhi Li, Qian Wang, Wenwei Zhang, Banglin Chen, Shuhua Li, Yi Pan, Xiaozeng You and Junfeng Bai
Chemical Communications 2016 vol. 52(Issue 45) pp:7241-7244
Publication Date(Web):04 May 2016
DOI:10.1039/C6CC03198F
Aiming to improve the acetylene (C2H2) storage capability of MOFs, we successfully designed NJU-Bai 17, a new analogue of MOF-505 with an inserted amide functional group which exhibits almost record high C2H2 uptakes of 222.4 cm3 g−1 at 296 K and 296 cm3 g−1 at 273 K under 1 bar. This result has been further supported by the determination of the heat of C2H2 adsorption and Grand Canonical Monte Carlo (GCMC) and first-principle calculations.
Co-reporter:Dandan Yuan, Xiaoling Shen, Wei Li and Shuhua Li
Physical Chemistry Chemical Physics 2016 vol. 18(Issue 24) pp:16491-16500
Publication Date(Web):25 May 2016
DOI:10.1039/C6CP01931E
Fragment-based quantum chemistry methods are either based on the many-body expansion or the inclusion–exclusion principle. To compare the applicability of these two categories of methods, we have systematically evaluated the performance of the generalized energy based fragmentation (GEBF) method (J. Phys. Chem. A, 2007, 111, 2193) and the electrostatically embedded many-body (EE-MB) method (J. Chem. Theory Comput., 2007, 3, 46) for medium-sized water clusters (H2O)n (n = 10, 20, 30). Our calculations demonstrate that the GEBF method provides uniformly accurate ground-state energies for 10 low-energy isomers of three water clusters under study at a series of theory levels, while the EE-MB method (with one water molecule as a fragment and without using the cutoff distance) shows a poor convergence for (H2O)20 and (H2O)30 when the basis set contains diffuse functions. Our analysis shows that the neglect of the basis set superposition error for each subsystem has little effect on the accuracy of the GEBF method, but leads to much less accurate results for the EE-MB method. The accuracy of the EE-MB method can be dramatically improved by using an appropriate cutoff distance and using two water molecules as a fragment. For (H2O)30, the average deviation of the EE-MB method truncated up to the three-body level calculated using this strategy (relative to the conventional energies) is about 0.003 hartree at the M06-2X/6-311++G** level, while the deviation of the GEBF method with a similar computational cost is less than 0.001 hartree. The GEBF method is demonstrated to be applicable for electronic structure calculations of water clusters at any basis set.
An unprecedented visible-light-induced direct C−H bond difluoroalkylation of aldehyde-derived hydrazones was developed. This reaction represents a new way to synthesize substituted hydrazones. The salient features of this reaction include difluorinated hydrazone synthesis rather than classical amine synthesis, extremely mild reaction conditions, high efficiency, wide substrate scope, ease in further transformations of the products, and one-pot syntheses. Mechanistic analyses and theoretical calculations indicate that this reaction is enabled by a novel aminyl radical/polar crossover mechanism, with the aminyl radical being oxidized into the corresponding aminyl cation through a single electron transfer (SET) process.
Chemistry - A European Journal 2016 Volume 22( Issue 36) pp:12910-12915
Publication Date(Web):
DOI:10.1002/chem.201601328
Abstract
Two perylene diimide (PDI) enantiomers (d/l-PDI) incorporating the d/l-alanine moiety have been designed and synthesized. d/l-PDI in chloroform displays bright-yellow fluorescence that is redshifted to orange-red when the solvent contains a methanol fraction of 99 vol %. No circular dichroism (CD) or circularly polarized luminescence (CPL) signals were observed for d/l-PDI enantiomers in CHCl3. Interestingly, the d/l-PDI enantiomers exhibit clear mirror-image Cotton effects and CPL emission in the aggregate state. The optical anisotropy factor (glum) is as high as 0.02 at fm=99 %, which can be attributed to self-assembly through intermolecular π–π interactions in the aggregate state.
Chemistry - A European Journal 2016 Volume 22( Issue 28) pp:9546-9550
Publication Date(Web):
DOI:10.1002/chem.201601819
Abstract
The debromination of vicinal dibromo compounds to generate alkenes usually requires harsh reaction conditions and the addition of catalysts. Just recently the visible-light-induced debromination of vicinal dibromo compounds emerged as a possible alternative to commonly used methods, but the substrate scope of this reaction is limited and a photocatalyst is necessary for the successful conversion of the starting compounds. A catalyst-free visible-light-induced debromination of vicinal dibromo compounds with a base-activated Hantzsch ester as photosensitizer is reported. The method has a wide substrate scope and a broad functional-group compatibility.
A series of chiral binaphthyl-based conjugated polymers enantiomers incorporating boron dipyrromethene (BODIPY) chromophore in the main chain backbone were designed and synthesized by Pd-catalyzed Sonogashira cross-coupling reaction. All of them can exhibit strong Cotton effects and circularly polarized luminescence (CPL) emission signals in THF solution. The CD absorption dissymmetry factors (gabs) and the luminescence dissymmetry factors (glum) can be regulated by tuning the dihedral angles of binaphthyl arising from different substitutions of BINOL hydroxyls. Interestingly, the chiral polymers can exhibit the gradual increase of both gabs and glum as the decrease of dihedral angles of the chiral binaphthyl moiety. This work can provide a new strategy for the development of CPL emission materials.
Co-reporter:Wei Li, Yunzhi Li, Ruochen Lin, and Shuhua Li
The Journal of Physical Chemistry A 2016 Volume 120(Issue 48) pp:9667-9677
Publication Date(Web):November 15, 2016
DOI:10.1021/acs.jpca.6b11193
We have extended the generalized energy-based fragmentation (GEBF) approach to localized excited states of large systems. In this approach, the excited-state energy of a large system could be expressed as the combination of the excited-state energies of “active subsystems”, which contains the chromophore center, and the ground-state energies of “inactive subsystems”. The GEBF approach has been implemented at the levels of time-dependent density functional theory (TDDFT) and approximate coupled cluster singles and doubles (CC2) method. Our results show that GEBF-TDDFT can reproduce the TDDFT excitation energies and solvatochromic shifts for large systems and that GEBF-CC2 could be used to validate GEBF-TDDFT result (with different functionals). The GEBF-TDDFT method is found to be able to provide satisfactory or reasonable descriptions on the experimental solvatochromic shifts for the n → π* transitions of acetone in various solutions, and the lowest π → π* transitions of pyridine and uracil in aqueous solutions.
The Journal of Physical Chemistry A 2016 Volume 120(Issue 17) pp:2700-2711
Publication Date(Web):April 13, 2016
DOI:10.1021/acs.jpca.5b10927
The generalized energy-based fragmentation (GEBF) approach for molecular crystals with periodic boundary condition (PBC) (denoted as PBC-GEBF) is extended to allow vibrational spectra of molecular crystals to be easily computed at various theory levels. Within the PBC-GEBF approach, the vibrational frequencies of a molecular crystal can be directly evaluated from molecular quantum chemistry calculations on a series of nonperiodic molecular systems. With this approach, the vibrational spectra of molecular crystals can be calculated with much reduced computational costs at various theory levels, as compared to those required by the methods based on periodic electronic structure theory. By testing the performance of the PBC-GEBF method for two molecular crystals (CO2 and imidazole), we demonstrate that the PBC-GEBF approach can reproduce the results of the methods based on periodic electronic structure theory in predicting vibrational spectra of molecular crystals. We apply the PBC-GEBF method at second-order Møller–Plesset perturbation theory (PBC-GEBF-MP2 in short) to investigate the vibrational spectra of the urea and ammonia borane crystals. Our results show that the PBC-GEBF-MP2 method can provide quite accurate descriptions for the observed vibrational spectra of the two systems under study.
Angewandte Chemie International Edition 2016 Volume 55( Issue 8) pp:2939-2943
Publication Date(Web):
DOI:10.1002/anie.201508698
Abstract
An unprecedented visible-light-induced direct C−H bond difluoroalkylation of aldehyde-derived hydrazones was developed. This reaction represents a new way to synthesize substituted hydrazones. The salient features of this reaction include difluorinated hydrazone synthesis rather than classical amine synthesis, extremely mild reaction conditions, high efficiency, wide substrate scope, ease in further transformations of the products, and one-pot syntheses. Mechanistic analyses and theoretical calculations indicate that this reaction is enabled by a novel aminyl radical/polar crossover mechanism, with the aminyl radical being oxidized into the corresponding aminyl cation through a single electron transfer (SET) process.
Co-reporter:Jiyang Zhao, Guoqiang Wang and Shuhua Li
Chemical Communications 2015 vol. 51(Issue 84) pp:15450-15453
Publication Date(Web):27 Aug 2015
DOI:10.1039/C5CC06808H
Density functional theory investigations reveal that the intramolecular additions of N–CN bonds to alkenes proceed in a novel asynchronous and concerted mechanism, while the intramolecular addition of O–CN bonds to alkenes may occur by both concerted and stepwise pathways.
Journal of Chemical Theory and Computation 2015 Volume 11(Issue 10) pp:4634-4643
Publication Date(Web):September 2, 2015
DOI:10.1021/acs.jctc.5b00495
A multireference second order perturbation theory based on a complete active space configuration interaction (CASCI) function or density matrix renormalized group (DMRG) function has been proposed. This method may be considered as an approximation to the CAS/A approach with the same reference, in which the dynamical correlation is simplified with blocked correlated second order perturbation theory based on the generalized valence bond (GVB) reference (GVB-BCPT2). This method, denoted as CASCI-BCPT2/GVB or DMRG-BCPT2/GVB, is size consistent and has a similar computational cost as the conventional second order perturbation theory (MP2). We have applied it to investigate a number of problems of chemical interest. These problems include bond-breaking potential energy surfaces in four molecules, the spectroscopic constants of six diatomic molecules, the reaction barrier for the automerization of cyclobutadiene, and the energy difference between the monocyclic and bicyclic forms of 2,6-pyridyne. Our test applications demonstrate that CASCI-BCPT2/GVB can provide comparable results with CASPT2 (second order perturbation theory based on the complete active space self-consistent-field wave function) for systems under study. Furthermore, the DMRG-BCPT2/GVB method is applicable to treat strongly correlated systems with large active spaces, which are beyond the capability of CASPT2.
Co-reporter:Tao Fang, Wei Li, Fangwei Gu, and Shuhua Li
Journal of Chemical Theory and Computation 2015 Volume 11(Issue 1) pp:91-98
Publication Date(Web):December 1, 2014
DOI:10.1021/ct500833k
We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals.
The reaction mechanism for the full hydrogenation of 2-phenyl-6-methyl-pyridine catalyzed by the Lewis acid C6F5(CH2)2B(C6F5)2 was investigated in detail by density functional theory calculations. Our calculations show that a plausible reaction pathway of the hydrogenation of pyridine contains five stages: (1) the generation of a new borane C6F5(CH2)2B(C6F5)2 from the hydroboration of the alkene, which forms a frustrated Lewis pair (FLP) with a pyridine; (2) the activation of H2 by FLP to yield an ion pair intermediate; (3) intramolecular hydride transfer from the boron atom to the pyridinium cation in the ion pair intermediate to produce the 1,4-dihydropyridine; (4) hydrogenation of the 1,4-dihydropyridine by the FLP to form the 1,4,5,6-tetrahydropyridine; (5) hydrogenation of the 1,4,5,6-tetrahydropyridine by the FLP to yield the final piperidine. The last two hydrogenation processes follow a similar pathway, which includes four steps: (a) proton transfer from the pyridinium moiety to the substrate; (b) dissociation of the newly generated pyridine; (c) hydride migration from the hydridoborate moiety to the protonated substrate to produce the hydrogenated product; (d) release of the hydrogenated product to regenerate the free borane. The full hydrogenation of pyridine is calculated to be exothermic by 16.9 kcal mol−1, relative to the starting reactants. The rate-limiting step is the proton transfer in the second hydrogenation step, with a free energy barrier of 28.2 kcal mol−1 in the gas phase (27.9 kcal mol−1 in toluene) at room temperature and 1.0 atm. Our results can account for the observed experimental facts.
Accounts of Chemical Research 2014 Volume 47(Issue 9) pp:2712
Publication Date(Web):May 29, 2014
DOI:10.1021/ar500038z
The generalized energy-based fragmentation (GEBF) approach provides a very simple way of approximately evaluating the ground-state energy or properties of a large system in terms of ground-state energies of various small “electrostatically embedded” subsystems, which can be calculated with any traditional ab initio quantum chemistry (X) method (X = Hartree–Fock, density functional theory, and so on). Due to its excellent parallel efficiency, the GEBF approach at the X theory level (GEBF-X) allows full quantum mechanical (QM) calculations to be accessible for systems with hundreds and even thousands of atoms on ordinary workstations. The implementation of the GEBF approach at various theoretical levels can be easily done with existing quantum chemistry programs.This Account reviews the methodology, implementation, and applications of the GEBF-X approach. This method has been successfully applied to optimize the structures of various large systems including molecular clusters, polypeptides, proteins, and foldamers. Such investigations could allow us to elucidate the origin and nature of the cooperative interaction in secondary structures of long peptides or the driving force of the self-assembly processes of aromatic oligoamides. These GEBF-based QM calculations reveal that the structures and stability of various complex systems result from a subtle balance of many types of noncovalent interactions such as hydrogen bonding and van der Waals interactions. The GEBF-based ab initio molecular dynamics (AIMD) method also allows the investigation of dynamic behaviors of large systems on the order of tens of picoseconds. It was demonstrated that the conformational dynamics of two model peptides predicted by GEBF-based AIMD are noticeably different from those predicted by the classical force field MD method.With the target of extending QM calculations to molecular aggregates in the condensed phase, we have implemented the GEBF-based multilayer hybrid models, which could provide satisfactory descriptions of the binding energies between a solute molecule and its surrounding waters and the chain-length dependence of the conformational changes of oligomers in aqueous solutions. A coarse-grained polarizable molecular mechanics model, furnished with GEBF-X dipole moments of subsystems, exhibits some advantages of treating the electrostatic polarization with reduced computational costs. We anticipate that the GEBF approach will continue to develop with the ultimate goal of studying complicated phenomena at mesoscopic scales and serve as a practical tool to elucidate the structure and dynamics of chemical and biological systems.
Co-reporter:Chenyang Zhang, Dandan Yuan, Yang Guo, and Shuhua Li
Journal of Chemical Theory and Computation 2014 Volume 10(Issue 12) pp:5308-5317
Publication Date(Web):October 21, 2014
DOI:10.1021/ct500551p
An efficient implementation of the local excitation approximation (LEA) of time-dependent density functional theory (TDDFT) or time-dependent Hartree–Fock, (TDHF) (or configuration interaction singles, CIS) method has been developed in this work. The LEA-TDDFT, -TDHF, and -CIS methods have been applied to investigate the solvatochromic shift of the n → π* vertical excitation energy of acetone in aqueous solution. The main idea of the LEA scheme is that only local electron excitations within a certain active region (called as chromophore) are treated to obtain the excitation energies for locally excited electronic states. We have proposed an efficient localization procedure to obtain regional localized molecular orbitals (RLMOs) localized on the chromophore subunit. To ensure the accuracy of the TDDFT, TDHF, and CIS schemes for the studied system, we choose one acetone and six nearest-neighboring waters as the active region for each acetone–water cluster. For acetone in aqueous solution, the LEA-TDDFT calculations on 600 acetone–water configurations (generated from molecular dynamics simulation) suggest that the blueshift in the n → π* vertical electronic excitation energy is 1621 ± 52 cm–1, which is in good agreement with the available experimental blue shift of 1500–1700 cm–1.
The Journal of Physical Chemistry A 2014 Volume 118(Issue 39) pp:8996-9004
Publication Date(Web):June 25, 2014
DOI:10.1021/jp501976x
An improved cluster-in-molecule (CIM) local correlation approach is developed to allow electron correlation calculations of large systems more accurate and faster. We have proposed a refined strategy of constructing virtual LMOs of various clusters, which is suitable for basis sets of various types. To recover medium-range electron correlation, which is important for quantitative descriptions of large systems, we find that a larger distance threshold (ξ) is necessary for highly accurate results. Our illustrative calculations show that the present CIM-MP2 (second-order Møller-Plesser perturbation theory, MP2) or CIM-CCSD (coupled cluster singles and doubles, CCSD) scheme with a suitable ξ value is capable of recovering more than 99.8% correlation energies for a wide range of systems at different basis sets. Furthermore, the present CIM-MP2 scheme can provide reliable relative energy differences as the conventional MP2 method for secondary structures of polypeptides.
Science China Chemistry 2014 Volume 57( Issue 1) pp:78-86
Publication Date(Web):2014 January
DOI:10.1007/s11426-013-5022-6
A linear scaling local correlation method, cluster-in-molecule (CIM) method, was developed in the last decade for large systems. The basic idea of the CIM method is that the electron correlation energy of a large system, within the Møller-Plesset perturbation theory (MP) or coupled cluster (CC) theory, can be approximately obtained from solving the corresponding MP or CC equations of various clusters. Each of such clusters consists of a subset of localized molecular orbitals (LMOs) of the target system, and can be treated independently at various theory levels. In the present article, the main idea of the CIM method is reviewed, followed by brief descriptions of some recent developments, including its multilevel extension and different ways of constructing clusters. Then, some applications for large systems are illustrated. The CIM method is shown to be an efficient and reliable method for electron correlation calculations of large systems, including biomolecules and supramolecular complexes.
Science China Chemistry 2014 Volume 57( Issue 10) pp:1393-1398
Publication Date(Web):2014 October
DOI:10.1007/s11426-014-5181-0
We describe an implementation of the cluster-in-molecule (CIM) resolution of the identity (RI) approximation second-order Møller-Plesset perturbation theory (CIM-RI-MP2), with the purpose of extending RI-MP2 calculations to very large systems. For typical conformers of several large polypeptides, we calculated their conformational energy differences with the CIM-RI-MP2 and the generalized energy-based fragmentation MP2 (GEBF-MP2) methods, and compared these results with the density functional theory (DFT) results obtained with several popular functionals. Our calculations show that the conformational energy differences obtained with CIM-RI-MP2 and GEBF-MP2 are very close to each other. In comparison with the GEBF-MP2 and CIM-RI-MP2 relative energies, we found that the DFT functionals (CAM-B3LYP-D3, LC-ωPBE-D3, M05-2X, M06-2X and ωB97XD) can give quite accurate conformational energy differences for structurally similar conformers, but provide less-accurate results for structurally very different conformers.
Chemical Communications 2013 vol. 49(Issue 15) pp:1542-1544
Publication Date(Web):07 Jan 2013
DOI:10.1039/C2CC38165F
Density functional theory investigations reveal that a cavitand with an introverted aldehyde group not only provides the host–guest interaction for preorganizing the substrate and stabilizing the hemiaminal intermediate, but also acts as an acid/base catalyst in the subsequent dehydration step in its reaction with a primary amine.
Complexes containing a Ru2n+ core (n = 4, 5 or 6) have been of great interest because of their variety of electronic configurations and magnetic properties. Herein, we report a novel homovalent Ru26+-based complex, (H2pip)2[Ru2(hedp)2Cl2]·6H2O (pip = piperazine) (1), isolated by the direct reaction of the mixed-valent Ru25+-based anion Ru2(hedp)23− [hedp = 1-hydroxyethylidenediphosphonate, CH3C(OH)(PO3)2] with oxidant peracetic acid under room temperature conditions. Magnetic measurements unambiguously confirm that this complex contains four unpaired electrons with a spin ground state of S = 2.
Co-reporter:Lina Xu, Weijie Hua, Shugui Hua, Jun Li, and Shuhua Li
The Journal of Organic Chemistry 2013 Volume 78(Issue 8) pp:3577-3582
Publication Date(Web):March 31, 2013
DOI:10.1021/jo4000509
We combined Monte Carlo simulations and density functional theory calculations to study the mechanism of the Diels–Alder reaction of p-quinone and cyclohexadiene catalyzed by a self-assembled molecular capsule. Our calculations show that the encapsulation of the reactants into the cage is driven by hydrogen-bonding interactions and π–π stacking interactions between two reactants and the capsule. The encapsulated Diels–Alder reaction at different locations inside the capsule may have quite different reactivity due to different guest–host interactions. A comparison of the free energy profiles of the Diels–Alder reaction in the capsule and in the bulk solution reveals that the Diels–Alder reaction in the capsule is accelerated because the host–guest interaction leads to a relatively smaller barrier for the cycloaddition step.
Co-reporter:Zhuangfei Kou, Jun Shen, Enhua Xu, and Shuhua Li
The Journal of Physical Chemistry A 2013 Volume 117(Issue 3) pp:626-632
Publication Date(Web):December 27, 2012
DOI:10.1021/jp309218q
We report an efficient implementation of the coupled cluster (CC) singles, doubles, and a hybrid treatment of triples based on the split virtual orbitals (SVO-CCSD(T)-h) method [J. Chem. Phys.2012, 136, 044101]. In this approach, virtual orbitals are split into two subsets, and correspondingly triple excitations are divided into active and inactive subsets. The active triple excitations are treated with the CCSDt (CC singles, doubles, and active triples) method, while the inactive triple excitations are treated with the CCSD(T) (CC singles, doubles, and perturbative triples) method. In the present work, the use of semicanonical molecular orbitals allows the CCSD(T)-like equations in SVO-CCSD(T)-h to be solved without iteration. As a result, the present SVO-CCSD(T)-h scheme does not need a large disk space to store the large number of triple excitation amplitudes, which is required by the original scheme. Test applications indicate that the present method can give results almost identical to those of the original scheme. The present method is then applied to investigate the reaction barriers for a number of simple reactions and spectroscopic constants including the equilibrium bond lengths and vibrational frequencies in several open-shell diatomic molecules. The SVO-CCSD(T)-h method is demonstrated to provide a significant improvement upon the CCSD(T) method in many cases.
We propose an improved fragmentation scheme for the generalized energy-based fragmentation (GEBF) approach, which improves the accuracy of the GEBF approach in total energy calculations and intermolecular interactions. The main modification is to introduce some two-fragment-centered primitive subsystems, which are neglected in the previous GEBF implementation. Numerical calculations demonstrate that the present GEBF approach can provide more accurate ground-state energies and intermolecular interactions. The present GEBF approach with the M06-2X functional and the cc-pVTZ basis set are employed to investigate the structures and binding energies in two dimeric species, which are related to pseudopolymorphism of a phenyleneethynylene-based π-conjugated molecule. A comparison of the binding free energies in a dimeric species and its corresponding model without CH⋅⋅⋅F contacts reveal that the substitution of fluorine atoms weakens the binding of monomers in the dimeric species formed by intermolecular OH⋅⋅⋅O hydrogen bonds, but strengthens the binding in the dimer formed by the π–π stacking interaction. Therefore, the CH⋅⋅⋅F contacts in these two dimeric species are demonstrated to play a less significant role.
Co-reporter:Jingui Duan, Zhen Yang, Junfeng Bai, Baishu Zheng, Yizhi Li and Shuhua Li
Chemical Communications 2012 vol. 48(Issue 25) pp:3058-3060
Publication Date(Web):12 Dec 2011
DOI:10.1039/C2CC16231H
An amide-inserted metal–organic framework (NJU-Bai3) presents high storage and high selectivity toward CO2 and combines these two interesting characters which strongly support our expectation that amide groups can significantly enhance the CO2 binding ability and selectivity of MOFs.
Co-reporter:Baishu Zheng, Zhen Yang, Junfeng Bai, Yizhi Li and Shuhua Li
Chemical Communications 2012 vol. 48(Issue 56) pp:7025-7027
Publication Date(Web):20 Jan 2012
DOI:10.1039/C2CC17593B
Two mesoporous and flexible acylamide-functionalized rht-type MOFs exhibit not only high excess unsaturation CO2 uptake (157 wt%) at 20 bar and 273 K, but also good selectivity of CO2/CH4 (8.6) and CO2/N2 (34.3). The advantages of acylamide groups for CO2 capture have been further confirmed by GCMC and first-principles calculations.
Physical Chemistry Chemical Physics 2012 vol. 14(Issue 21) pp:7854-7862
Publication Date(Web):12 Mar 2012
DOI:10.1039/C2CP23916G
A refined cluster-in-molecule (CIM) method for local correlation calculations of large molecules is presented. In the present work, two new strategies are introduced to further improve the CIM approach: (1) Some medium-range electron correlation energies, which are neglected in the previous CIM approach, are taken into account. (2) A much simpler procedure using only a distance threshold is used to construct various clusters. To cover the medium-range correlation effect as much as possible, some two-atom-centered clusters are built, in addition to one-atom-centered clusters. Our test calculations at the second order perturbation theory (MP2) level show that the refined CIM method can recover about 99.9% of the conventional MP2 correlation energy using an appropriate distance threshold. The accuracy of the present CIM method is capable of providing reliable relative energies of medium-sized systems such as polyalanines with 10 residues, and water molecules with 50 water molecules. For polyalanines with up to 30 residues, we have demonstrated that the computational cost of the CIM-MP2 calculation increases linearly with the molecular size, but the required memory and disc-space do not need to increase for large systems. The improved CIM method has been used to compute the relative energy of ice-like (H2O)96 clusters (with 2400 basis functions) and to predict the dimerization energy of a double-helical foldamer (with 2330 basis functions). The present CIM method is expected to be a practical local correlation method for describing the relative energies of large systems.
Co-reporter:Zhuangfei Kou, Jun Shen, Enhua Xu, Shuhua Li
Chemical Physics 2012 Volume 401() pp:113-118
Publication Date(Web):5 June 2012
DOI:10.1016/j.chemphys.2011.10.023
Abstract
A coupled cluster singles, doubles, and a hybrid treatment of triples [denoted as CCSD(T)-h] has been applied to investigate the equilibrium geometries and harmonic frequencies of five diatomic open-shell molecules, bond breaking potential energy surfaces in C2 and , and the twisting potential energy surface of ethylene. In the present work, CCSD(T)-h calculations are based on the restricted or restricted open-shell Hartree–Fock (RHF or ROHF) reference. A general procedure for constructing the active RHF or ROHF orbitals is proposed. A comparison of CCSD(T)-h with other CC methods show that for all systems CCSD(T)-h is an excellent approximation to CCSDT, being much better than CCSD(T) especially when a molecule exhibits strong multireference character.
Density functional theory calculations were performed to elucidate the mechanism of dehydrogenative coupling of primary alcohols and amines mediated by a PNN–Ru(II) hydride complex (PNN = (2-(di-tert-butylphosphinomethyl)-6-(diethylaminomethyl)pyridine)). A plausible reaction pathway was proposed which contains three stages: (1) The alcohol dehydrogenation reaction to generate the aldehyde and H2; (2) The aldehyde-amine condensation reaction to form the hemiaminal intermediate; (3) The dehydrogenation process of the hemiaminal intermediate to yield the final amide product with the liberation of H2. The first and third stages occur via a similar pathway: (a) Proton transfer from the substrate to the PNN ligand; (b) Intramolecular rearrangement of the deprotonated substrate to form an anagostic complex; (c) Hydride transfer from the deprotonated substrate to the Ru center to yield the trans-dihydride intermediate and the aldehyde (or amide); (d) Benzylic proton migration from the PNN ligand to the metal center forming a dihydrogen complex and subsequent H2 liberation to regenerate the catalyst. In all these steps, the metal–ligand cooperation plays an essential role. In proton transfer steps (a) and (d), the metal–ligand cooperation is achieved through the aromatization/dearomatization processes of the PNN ligand. While in steps (b) and (c), their collaboration are demonstrated by the formation of an anagostic interaction between Ru and the C–H bond and two ionic hydrogen bonds supported by the PNN ligand.
Co-reporter:Jun Shen, Enhua Xu, Zhuangfei Kou and Shuhua Li
Physical Chemistry Chemical Physics 2011 vol. 13(Issue 19) pp:8795-8804
Publication Date(Web):29 Mar 2011
DOI:10.1039/C0CP01103G
Here we review the basic formalism, implementation details, and performance of two newly developed coupled cluster (CC) methods based on the unrestricted Hartree–Fock (UHF) reference for treating molecules with multireference character. These two approaches can be considered to be approximations to the CC singles, doubles, and triples (CCSDT) method. The key concept of these two approaches is the corresponding orbitals, which are unitary transformations of canonical UHF molecular orbitals so that all spin orbitals are grouped into unique orbital pairs. In one approach called CCSDT(5P), a subset of triple excitations involving up to five-pair indices is included. In another approach called CCSD(T)-h, the contribution of connected triple excitations is treated in a hybrid way. With the concept of active corresponding orbitals, triple excitations can be automatically partitioned into two subsets, and the amplitudes of these two subsets are determined via solving different equations. Both CCSD(T)-h and CCSDT(5P) computationally scale as the seventh power of the system size. A survey of a number of applications demonstrates that CCSD(T)-h is an excellent approximation to the full CCSDT method, and CCSDT(5P) provides a good approximation to CCSDT for single-bond breaking processes. The overall performance of CCSDT(5P) is less accurate than that of CCSD(T)-h, but significantly better than that of the widely used CCSD(T).
Co-reporter:Shugui Hua, Lina Xu, Wei Li, and Shuhua Li
The Journal of Physical Chemistry B 2011 Volume 115(Issue 39) pp:11462-11469
Publication Date(Web):August 22, 2011
DOI:10.1021/jp203423w
We have employed the generalized energy-based fragmentation (GEBF) approach to investigate the structures, energies, and enthalpies of α-helices, 310-helices, and β-strands for capped polyalanines, acetyl(ala)NNH2, with N values from 8 to 40 at several theoretical levels. The M06-2X functional is demonstrated to be much more accurate than the B3LYP functional for peptides under study. On the basis of the GEBF-M06-2X results, we find that α-helices are more stable than the corresponding 310-helices for all peptides with N ≥ 10. The cooperative interaction in both helices have not reached their asymptotic limits even for N = 40. By comparing the performance of the M06-2X, B3LYP, and the van der Waals corrected B3LYP, we show that both electrostatic and van der Waals interactions are essential for describing the cooperative interaction in long helices. In addition, the greater cooperativity of α-helices over 310-helices in long helices is found to originate mainly from the much stronger van der Waals interaction in α-helices.
We performed a computational investigation to understand the conformational preferences of four short peptides in a self-assembled cage based on the experimental work by Y. Hatakeyama et al. (Angew. Chem. Int. Ed.2009, 48, 8695). For this purpose, we combined molecular dynamics simulations, Monte Carlo simulations, and quantum mechanical calculations to obtain energies and structures for several low-lying conformers of four peptides and the corresponding peptide-cage inclusion complexes. Our calculations at both B3LYP and MP2 levels show that for each peptide, the corresponding conformation within the host (as revealed by the crystal structure) does not represent the lowest-energy conformation of this peptide in vacuum. By comparing some low-lying conformers in vacuum and in the cavity (for the same peptide), we found that the cage has a significant influence on the conformational propensities of peptides. First, one carbonyl oxygen of each peptide tends to bind to one Zn (II) atom of the cage, forming a ZnO bond. The formation of this bond leads to significant charge transfer from the cage to the peptide. Second, this ZnO bond causes the peptide to go through some local conformational changes. For larger peptides, such as penta- and hexapeptides, our calculations also show that some of their conformers must undergo significant structural changes, due to the confinement of the host. This computational study reveals the noticeable influence of the guest–host interaction on the conformational preferences of short peptides.
Co-reporter:Zhen Yang, Shugui Hua, Weijie Hua, and Shuhua Li
The Journal of Physical Chemistry B 2011 Volume 115(Issue 25) pp:8249-8256
Publication Date(Web):June 2, 2011
DOI:10.1021/jp2030736
Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been carried out to investigate the structures of the neutral (H2O)21 and protonated H+(H2O)21 clusters confined in the crystal hosts. The influence of other cocrystallized species and the local electrostatic environments of the crystal hosts on the structures of water clusters has been analyzed. For the neutral (H2O)21 cluster in the tetrahedral host, its low-lying structures are found to exist as a dodecahedral cage with one interior water molecule, which is in good accord with the corresponding X-ray data. The confined (H2O)21 cluster possesses the main structural features of the lowest-energy structure of the free (H2O)21 cluster in the gas phase. For the protonated H+(H2O)21 cluster confined in the cubic cavity, its low-lying structures are found to have a common hexahedral (H2O)20 shell, which is consistent with the experimental X-ray structure, but the position of the additional H2O (or the H3O+ ion) in different low-lying structures is different, while the H3O+ ion is situated at the center of the cage in the corresponding X-ray structure. The overall shape of the confined H+(H2O)21 cluster is significantly different from that of the free cluster in the gas phase, and the confined cluster has much less intrinsic hydrogen bonds (H-bonds) than the free cluster, due to the need to form extrinsic H-bonds with acetonitrile molecules in the crystal host. The local electrostatic environment of the crystal host is found to exert a negligible influence on the structure of the (H2O)21 cluster but play a significant role in modulating the structure of the H+(H2O)21 cluster. This may be attributed to the fact that the protonated water cluster is much more easily polarized by the external electrostatic field of the crystal host than the neutral water cluster.
Density functional theory calculations have been performed to investigate the molecular mechanism of the hydrogenation reactions of 1,1-diphenylethylene and myrcene catalyzed by the actual calcium hydride catalyst, CaH(dipp-nacnac)(thf) (dipp-nacnac = CH{(CMe)(2,6-iPr2−C6H3N)}2). The hydrogenation reactions of these two alkenes proceed via a similar pathway, which includes three steps. First, the hydride migrates from the calcium center to one olefinic carbon in the substrate. Then, the hydride transfer product can easily transform into a key ion-pair intermediate. This intermediate provides an intramolecular frustrated Lewis pair, in which the calcium center acts as a Lewis acid, and one olefinic carbon acts as a Lewis base. Next, the H−H bond is heterolytically cleaved by this frustrated Lewis pair through a concerted Lewis acid−Lewis base mechanism, producing the hydrogenation product and regenerating the catalyst. For these two reactions, the rate-limiting step is the hydride transfer step, with free energy barriers of 29.2 kcal for both substrates. In addition, our calculations indicate that the hydrogenation reaction of 1,1-diphenylethylene catalyzed by the analogous strontium hydride complex may readily occur, but the similar magnesium-mediated hydrogenation reaction is less likely to take place under similar conditions as adopted by the calcium hydride catalyst. The results can give satisfactory descriptions of experimental facts observed for these two hydrogenation reactions. The hydrogenation mechanism proposed here is different from that of the late transition metal-catalyzed alkene hydrogenation or the organolanthanide-catalyzed alkene hydrogenation.
The molecular mechanism of H2 activation by two transition metal thiolate complexes [Cp*M(PMe3)(SDmp)](BArF4) (M = Ir, Rh) (Ohki, Y; Sakamoto, M; Tatsumi, K. J. Am. Chem. Soc., 2008, 130, 11610–11611) has been investigated using density functional theory calculations. According to our calculations, the reaction of the iridium thiolate complex with H2 is likely to proceed through the following steps: (1) the oxidative addition of H2 to the iridium center to generate a dihydride intermediate; (2) the reductive elimination of one Ir-bound hydrogen to produce the hydride thiol product. For the rhodium thiolate complex, its reaction with H2 is to form the dihydrogen intermediate first, and then the H–H bond is heterolytically cleaved at the Rh–S bond via a four-center transition state to yield the hydride thiol product. The rate-determining step is the oxidative addition step (with a barrier of 18.0 kcal/mol in the solvent) for the iridium complex, and the formation of the dihydrogen complex (with a barrier of 13.9 kcal/mol in the solvent) for the rhodium complex. The calculated free energy profiles for both metal thiolate complexes can reasonably account for the observed reversible H2 activation by two metal thiolate complexes under mild conditions.
Chinese Journal of Chemistry 2010 Volume 28( Issue 1) pp:41-49
Publication Date(Web):
DOI:10.1002/cjoc.201090033
Abstract
The mechanism of a typical Petasis-type boronic mannich reaction (the styrylboronic acid, dibenzylamine, and α-hydroxylpropionaldehyde) has been investigated using density functional theory calculations. According to our calculations, the reaction is most likely to proceed through the following steps: 1) the nucleophilic addition of the amine to the aldehyde to form the carbinolamine; 2) the dehydration of the carbinolamine; 3) the formation of the tetra-coordinated borate intermediate; 4) the CC bond formation by the intramolecular transfer of the styryl group; 5) the hydrolysis of the resulting intermediate to give the final products. The highest point on the energy profile is the transition state for the CC bond formation (118.8 kJ·mol−1 above the reactants in ethanol). Our results can give reasonable explanations on some experimental facts observed for many Petasis-type boronic Mannich reactions.
Co-reporter:Zhen Yang, Shugui Hua, Weijie Hua and Shuhua Li
The Journal of Physical Chemistry A 2010 Volume 114(Issue 34) pp:9253-9261
Publication Date(Web):July 29, 2010
DOI:10.1021/jp1038267
Based on a large database of local minima obtained with the polarizable AMOEBA potential, the generalized energy-based fragmentation (GEBF) approach is applied to locate low-lying structures of water clusters (H2O)n in the range n = 20−30, at the B3LYP and MP2 levels. Our results show that the relative stabilities of isomers predicted by the AMOEBA empirical potential differ noticeably from those predicted by GEBF-B3LYP/6-311++G(d,p) and GEBF-MP2/6-311++G(3df,2p) calculations. From GEBF-B3LYP energies with zero-point vibrational energy corrections, one can see that for water clusters in the range n = 20−30 the transition from one-centered to two-centered cage structure occurs at n = 26. With increasing cluster size, the number of H-bonds per water molecule in the lowest-energy structures shows a gradually increasing trend, and the proportion of four-coordinated water molecules gradually increases, as expected for large water clusters. Based on GEBF-MP2/6-311++G(3df,2p) energies (instead of GEBF-B3LYP/6-311++G(d,p) energies), different lowest-energy structures can be found for six cluster sizes in the range n = 20−30, suggesting the significance of the dispersion interaction in determining the relative energies of low-lying water clusters.
Science China Chemistry 2010 Volume 53( Issue 2) pp:289-296
Publication Date(Web):2010 February
DOI:10.1007/s11426-010-0034-y
The performances of several multireference electronic structure methods including complete active space self-consistent field (CASSCF)-based second-order perturbation theory (CASPT2), multireference configuration interaction with single and double excitations (MR-CISD), MR-CISD with the Davidson correction (MR-CISD+Q), and the CASSCF-based block-correlated coupled cluster method (CAS-BCCC4) we developed recently are compared by applying them to study several different chemical problems involving computation of ground state potential energy surfaces, the singlet-triplet gaps in diradicals, reaction barriers, and the excitation energies of low-lying excited states. Comparison with the results from other highly accurate theoretical methods or the available experimental data demonstrate that for all the problems studied, the overall performance of CAS-BCCC4 is competitive with that of MR-CISD+Q, and better than that of CASPT2 and MR-CISD methods. Thus the CAS-BCCC4 approach is expected to be a promising theoretical method for quantitative descriptions of the electronic structures of molecules with noticeable multireference character.
The Journal of Physical Chemistry A 2010 Volume 114(Issue 31) pp:8126-8134
Publication Date(Web):July 19, 2010
DOI:10.1021/jp103074f
An efficient implementation of the generalized energy-based fragmentation (GEBF) approach (Li, W.; Li, S.; Jiang, Y. J Phys. Chem. A 2007, 111, 2193) for treating a wide range of large molecules is presented. In this implementation, the fragmentation process can be automatically done for a general molecule, with only some functional groups defined by users. A new and fast scheme is designed for the generation of various subsystems and the derivation of their coefficients. The newly implemented GEBF approach has been applied to several large molecules including proteins, nucleic acids, and supermolecules with fused aromatic rings. Test calculations within the Hartree−Fock (HF) and density functional theory (DFT) framework demonstrate that the GEBF approach can provide reasonably accurate ground-state energies and optimized structures, which are in good agreement with those from conventional HF or DFT calculations. The GEBF approach implemented in this work can now be employed by nonexpert users to compute energies, optimized structures, and some molecular properties at various ab initio levels for a broad range of large molecules on ordinary PC workstations.
Density functional theory calculations have been carried out to explore the mechanism of the H2 activation by the (PNP)Ir(C6H5) complex. Our calculations show that the reaction is most likely to go though three steps. The first step (also the rate-determining step) involves the proton transfer from the benzylic position of the PNP ligand to the metal center to form an Ir(III) hydride intermediate, accompanied by the dearomatization of the PNP ligand. Second, H2 is coordinated to the metal of this Ir(III) intermediate to form a molecular hydrogen complex. Finally, the H−H bond is heterolytically cleaved to produce the final trans-dihydride product, in which the benzylic carbon is protonated, and the PNP ligand is rearomatized. Thus, the H2 activation by the Ir(I) complex actually involves an Ir(III) hydride complex as a key intermediate. The Ir center and the PNP ligand cooperate in a synergistic manner in the H2 activation process. The above molecular mechanism could provide reasonable explanations for known experimental facts.
The Journal of Physical Chemistry A 2009 Volume 113(Issue 7) pp:1335-1342
Publication Date(Web):January 26, 2009
DOI:10.1021/jp8071525
The generalized energy-based fragmentation (GEBF) approach has been implemented to extend the applications of density function theory (DFT) with empirical van der Waals (vdW) correction (Wu, Q.; Yang, W. T. J. Chem. Phys.2002, 116, 515.) to large supramolecular systems with extensive π−π stacking interactions. This mixed approach, DFT(vdW)-GEBF, is applied to investigate the energies and structures of several aromatic oligoamide foldamers. Our calculations show that the formation of single helical structures is mainly driven by the stacking interaction between neighboring aromatic rings, further stabilized by the intramolecular hydrogen bonds of the backbone. The dimerization of two single helical strands to form the double helical structure is an energetically favorable process, which is mainly driven by extensive interstrand aromatic−aromatic interactions. However, the dimerization energy tends to decrease significantly for longer oligomeric strands.
Journal of Molecular Structure: THEOCHEM 2009 Volume 899(1–3) pp:61-70
Publication Date(Web):15 April 2009
DOI:10.1016/j.theochem.2008.12.007
The molecular mechanism of the reaction of 2-heptanone and trimethylsilyl cyanide (TMSCN) catalyzed by the bifunctional titanium catalyst (to produce cyanohydrin) has been investigated using density functional theory calculations. With the bifunctional titanium catalyst, the reaction is likely to proceed through the following steps sequentially: (1) the isomerization of the cyano group into the isocyano group at the Si center of TMSCN; (2) the addition of the isocyano group to the ketone; (3) the silylation of the cyanoalkoxyl group to give the product. Our calculations reveal that the phosphine oxide group (as the Lewis base) and the titanium atom (as the Lewis acid) in the catalyst work cooperatively to promote the nucleophilic addition of the isocyano group to the ketone, and the silylation of the resulting cyanoalkoxyl group to form the product, respectively.
Density functional theory calculations have been carried out to investigate the possible reaction mechanisms for the reversible dihydrogen activation catalyzed by a phosphine−borane compound, (C 6H 2Me 3) 2P(C 6F 4)B(C 6F 5) 2 (Welch, G. C.; Juan, R. R. S; Masuda, J. D.; Stephan, D. W. Science. 2006, 314, 1124−1126). The present calculations show that an unusual concerted Lewis acid−Lewis base mechanism is more favorable than the proton transfer or hydride transfer mechanisms suggested previously. In the concerted Lewis acid−Lewis base mechanism, the H−H heterolytic cleavage is achieved through the simultaneous electron transfer from the lone-pair orbital of the Lewis base P center to the σ* orbital of H 2 and from the σ orbital of H 2 to the empty orbital of the Lewis acid B center. The solvent is found to dramatically change the potential energy surface. The proposed mechanism can account well for the bimolecular H−D exchange process observed in deuteration experiments and the experimental fact that the H 2 activation is reversible at mild conditions.
Co-reporter:Jun Shen, Tao Fang, Shuhua Li and Yuansheng Jiang
The Journal of Physical Chemistry A 2008 Volume 112(Issue 48) pp:12518-12525
Publication Date(Web):November 12, 2008
DOI:10.1021/jp807183m
The spatial orbital formulations of block correlated coupled cluster (BCCC) theory with a general CASSCF reference function (CAS-BCCC in short) is derived and an efficient implementation of this approach at the four-block correlation level (abbreviated CAS-BCCC4) is reported. We have applied the CAS-BCCC4 approach to investigate energy barriers for several reactions (the ring-opening isomerization of the cyclopropyl radical, cyclobutene, cyclobutadiene, and bicyclo[3.1.0]hex-2-ene), spectroscopic constants in several multibond diatomic molecules (C2, O2, CO, and N2), and singlet−triplet gaps in two diradicals (trimethylenemethane and oxyallyl). A comparison of CAS-BCCC4 results with the experimental data or other theoretical estimates shows that the present approach can provide very satisfactory descriptions for all the studied systems.
Science China Chemistry 2008 Volume 51( Issue 12) pp:1197-1202
Publication Date(Web):2008 December
DOI:10.1007/s11426-008-0139-8
The block correlated coupled cluster (BCCC) method, with the complete active-space self-consistent-field (CASSCF) reference function, has been applied to investigating the singlet-triplet gaps in several substituted carbenes including four halocarbenes (CHCl, CF2, CCl2, and CBr2) and two hydroxycarbenes (CHOH and C(OH)2). A comparison of our results with the experimental data and other theoretical estimates shows that the present approach can provide quantitative descriptions for all the studied carbenes. It is demonstrated that the CAS-BCCC method is a promising theoretical tool for calculating the electronic structures of diradicals.
Co-reporter:Jun Shen, Tao Fang, Weijie Hua and Shuhua Li
The Journal of Physical Chemistry A 2008 Volume 112(Issue 20) pp:4703-4709
Publication Date(Web):April 24, 2008
DOI:10.1021/jp7118907
The spatial orbital formulations of block-correlated coupled cluster (BCCC) theory with a complete active-space self-consistent-field (CASSCF) reference function and its efficient implementation is presented. In the present implementation, the cluster operator is truncated to the four-block correlation level, and the CASSCF(2,2) reference function is assumed (thus, the method is abbreviated as CAS-BCCC4). We have applied this method to investigate the spectroscopic constants in seven single-bond diatomic molecules (LiH, HF, HCl, Li2, F2, ClF, and Cl2) and the singlet−triplet gaps in a series of typical diradicals, including carbon, oxygen, and silicon atoms, methylene (CH2) and its isovalent species (NH2+, SiH2, and PH2+), and three benzyne isomers. A comparison of our results with the experimental data or other theoretical estimates shows that the present approach can provide quantitative descriptions for all of the studied systems.
The Journal of Physical Chemistry C 2008 Volume 112(Issue 43) pp:16938-16944
Publication Date(Web):October 4, 2008
DOI:10.1021/jp803566t
The possible mechanisms for the “fast” selective catalytic reduction (SCR) of nitrogen oxides with ammonia over Fe-exchanged zeolites have been investigated with density functional theory calculations. Three mechanisms studied in this work include (1) the reaction of (NO + NO2) with NH3 in gas phase (via N2O3), (2) the decomposition of NH4NO2, and (3) the reaction of (NO + NO2) with NH3 catalyzed by the Fe-exchanged zeolites (modeled by the Z−[FeO]+site). For the mechanisms 1 and 2, our calculations show that the activation barriers of the rate-limiting steps are 22.5 and 24.0 kcal/mol, respectively. In these two mechanisms, the key intermediate is NH2NO, which decomposes into the final products N2 and H2O. For mechanism 3, we find that the key intermediate NH2NO can be formed from the reaction of NO with NH3 on the [FeO]+ site, and the resulting reduced active site [FeOH]+ can be reoxidized by NO2 and NH3 to regenerate the active site. The formation of NH2NO is calculated to be exergonic by 34.2 kcal/mol and with an activation barrier of 3.0 kcal/mol. The regeneration of the active site involves an activation barrier of 32.0 kcal/mol. Mechanisms 1 and 2 may be responsible for the “fast SCR” of NOx with NH3 observed at lower temperatures (below 373 K), and mechanism 3 may provide a possible explanation on the high activity of the “fast SCR” of NOx with NH3 over the Fe-exchanged zeolites at higher temperatures.
The macroscopic viscoelastic properties of a physical hydrogel are reversibly modulated by tuning the microscopic hydrogen-bonding interactions with pH. The hydrogel forms at a rather low concentration of the multi-pyridyl-based gelator, N, N′, N″-tris(3-pyridyl)trimesic amide. The yield stress of the hydrogel is greatly enhanced from 10 to 769 Pa by changing the pH from 7.0 to 5.0. At pH 7.0, the amide molecules are assembled into an ordered structure as a result of the hydrogen bonds between the amide N–H bond and the nitrogen on the pyridyl group (N–H…Py). Fourier transform (FT) IR spectroscopy indicates that hydrogen bonds of N–H…Py are partially broken because the pyridyl groups are partly protonated at pH 5.0. This condition leads to a highly branched and homogeneous fibrillar network, which is confirmed by X-ray diffraction (XRD) measurements and field-emission scanning electron microscopy (FESEM) images. Highly branched fibrillar networks create more compartments and greatly increase the interfacial tension that is required to hold the solvent in the gel, thereby increasing the yield stress to 769 Pa. By further increasing the acidity of the hydrogel to pH < 3.0, the gel becomes a sol. Both the change in the viscoelastic properties and the sol–gel transition are reversible and controllable in the material.
Physical Chemistry Chemical Physics 2007 vol. 9(Issue 25) pp:3304-3311
Publication Date(Web):18 May 2007
DOI:10.1039/B700161D
Density functional theory calculations were carried out to investigate the reaction mechanism of selective catalytic reduction of nitrogen oxides by ammonia in the presence of oxygen at the Brønsted acid sites of H-form zeolites. The Brønsted acid site of H-form zeolites was modeled by an aluminosilicate cluster containing five tetrahedral (Al, Si) atoms. A low-activation-energy pathway for the catalytic reduction of NO was proposed. It consists of two successive stages: first NH2NO is formed in gas phase, and then is decomposed into N2 and H2O over H-form zeolites. In the first stage, the formation of NH2NO may occur via two routes: (1) NO is directly oxidized by O2 to NO2, and then NO2 combines with NO to form N2O3, which reacts with NH3 to produce NH2NO; (2) when NO2 exceeds NO in the content, NO2 associates with itself to form N2O4, and then N2O4 reacts with NH3 to produce NH2NO. The second stage was suggested to proceed with low activation energy via a series of synergic proton transfer steps catalyzed by H-form zeolites. The rate-determining step for the whole reduction of NOx is identified as the oxidation of NO to NO2 with an activation barrier of 15.6 kcal mol−1. This mechanism was found to account for many known experimental facts related to selective catalytic reduction of nitrogen oxides by ammonia over H-form zeolites.
Physical Chemistry Chemical Physics 2007 - vol. 9(Issue 25) pp:NaN3311-3311
Publication Date(Web):2007/05/18
DOI:10.1039/B700161D
Density functional theory calculations were carried out to investigate the reaction mechanism of selective catalytic reduction of nitrogen oxides by ammonia in the presence of oxygen at the Brønsted acid sites of H-form zeolites. The Brønsted acid site of H-form zeolites was modeled by an aluminosilicate cluster containing five tetrahedral (Al, Si) atoms. A low-activation-energy pathway for the catalytic reduction of NO was proposed. It consists of two successive stages: first NH2NO is formed in gas phase, and then is decomposed into N2 and H2O over H-form zeolites. In the first stage, the formation of NH2NO may occur via two routes: (1) NO is directly oxidized by O2 to NO2, and then NO2 combines with NO to form N2O3, which reacts with NH3 to produce NH2NO; (2) when NO2 exceeds NO in the content, NO2 associates with itself to form N2O4, and then N2O4 reacts with NH3 to produce NH2NO. The second stage was suggested to proceed with low activation energy via a series of synergic proton transfer steps catalyzed by H-form zeolites. The rate-determining step for the whole reduction of NOx is identified as the oxidation of NO to NO2 with an activation barrier of 15.6 kcal mol−1. This mechanism was found to account for many known experimental facts related to selective catalytic reduction of nitrogen oxides by ammonia over H-form zeolites.
The molecular mechanism of H2 activation by two transition metal thiolate complexes [Cp*M(PMe3)(SDmp)](BArF4) (M = Ir, Rh) (Ohki, Y; Sakamoto, M; Tatsumi, K. J. Am. Chem. Soc., 2008, 130, 11610–11611) has been investigated using density functional theory calculations. According to our calculations, the reaction of the iridium thiolate complex with H2 is likely to proceed through the following steps: (1) the oxidative addition of H2 to the iridium center to generate a dihydride intermediate; (2) the reductive elimination of one Ir-bound hydrogen to produce the hydride thiol product. For the rhodium thiolate complex, its reaction with H2 is to form the dihydrogen intermediate first, and then the H–H bond is heterolytically cleaved at the Rh–S bond via a four-center transition state to yield the hydride thiol product. The rate-determining step is the oxidative addition step (with a barrier of 18.0 kcal/mol in the solvent) for the iridium complex, and the formation of the dihydrogen complex (with a barrier of 13.9 kcal/mol in the solvent) for the rhodium complex. The calculated free energy profiles for both metal thiolate complexes can reasonably account for the observed reversible H2 activation by two metal thiolate complexes under mild conditions.
Chemical Communications 2013 - vol. 49(Issue 15) pp:NaN1544-1544
Publication Date(Web):2013/01/07
DOI:10.1039/C2CC38165F
Density functional theory investigations reveal that a cavitand with an introverted aldehyde group not only provides the host–guest interaction for preorganizing the substrate and stabilizing the hemiaminal intermediate, but also acts as an acid/base catalyst in the subsequent dehydration step in its reaction with a primary amine.
Co-reporter:Yunzhi Li, Guoqiang Wang, Wei Li, Yue Wang and Shuhua Li
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 27) pp:NaN17520-17520
Publication Date(Web):2017/06/12
DOI:10.1039/C7CP03584E
A refined QM/MM approach demonstrated that a monomer model is suitable for describing the emission spectra of crystals without the π⋯π stacking interaction. Whereas for the crystals with notable intermolecular π⋯π stacking interaction, the most stable trimer model (or at least a dimer model) should be used for accurately describing the corresponding emission spectra. This approach is applied to understand the emission properties of two kinds of organic polymorphs.
Co-reporter:Pan Xu, Guoqiang Wang, Zhongkai Wu, Shuhua li and Chengjian Zhu
Chemical Science (2010-Present) 2017 - vol. 8(Issue 2) pp:NaN1308-1308
Publication Date(Web):2016/10/07
DOI:10.1039/C6SC03888C
A novel and straightforward strategy for functionalized 1H-indazoles is realized by the Rh(III)-catalyzed double C–H activation and C–H/C–H cross coupling of readily available aldehyde phenylhydrazones. The reaction is scalable and various 1H-indazoles could be afforded in moderate to high yields with good functional-group compatibility. Mechanism experiments and DFT calculations suggest the distinctive Rh(III)-catalyzed C–H/C–H cross coupling reaction underwent a cascade C(aryl)–H bond metalation, C(aldhyde)–H bond insertion and reductive elimination process.
Co-reporter:Mingxing Zhang, Bin Li, Yunzhi Li, Qian Wang, Wenwei Zhang, Banglin Chen, Shuhua Li, Yi Pan, Xiaozeng You and Junfeng Bai
Chemical Communications 2016 - vol. 52(Issue 45) pp:NaN7244-7244
Publication Date(Web):2016/05/04
DOI:10.1039/C6CC03198F
Aiming to improve the acetylene (C2H2) storage capability of MOFs, we successfully designed NJU-Bai 17, a new analogue of MOF-505 with an inserted amide functional group which exhibits almost record high C2H2 uptakes of 222.4 cm3 g−1 at 296 K and 296 cm3 g−1 at 273 K under 1 bar. This result has been further supported by the determination of the heat of C2H2 adsorption and Grand Canonical Monte Carlo (GCMC) and first-principle calculations.
Co-reporter:Jiyang Zhao, Guoqiang Wang and Shuhua Li
Chemical Communications 2015 - vol. 51(Issue 84) pp:NaN15453-15453
Publication Date(Web):2015/08/27
DOI:10.1039/C5CC06808H
Density functional theory investigations reveal that the intramolecular additions of N–CN bonds to alkenes proceed in a novel asynchronous and concerted mechanism, while the intramolecular addition of O–CN bonds to alkenes may occur by both concerted and stepwise pathways.
Co-reporter:Jingui Duan, Zhen Yang, Junfeng Bai, Baishu Zheng, Yizhi Li and Shuhua Li
Chemical Communications 2012 - vol. 48(Issue 25) pp:NaN3060-3060
Publication Date(Web):2011/12/12
DOI:10.1039/C2CC16231H
An amide-inserted metal–organic framework (NJU-Bai3) presents high storage and high selectivity toward CO2 and combines these two interesting characters which strongly support our expectation that amide groups can significantly enhance the CO2 binding ability and selectivity of MOFs.
Co-reporter:Baishu Zheng, Zhen Yang, Junfeng Bai, Yizhi Li and Shuhua Li
Chemical Communications 2012 - vol. 48(Issue 56) pp:NaN7027-7027
Publication Date(Web):2012/01/20
DOI:10.1039/C2CC17593B
Two mesoporous and flexible acylamide-functionalized rht-type MOFs exhibit not only high excess unsaturation CO2 uptake (157 wt%) at 20 bar and 273 K, but also good selectivity of CO2/CH4 (8.6) and CO2/N2 (34.3). The advantages of acylamide groups for CO2 capture have been further confirmed by GCMC and first-principles calculations.
The reaction mechanism for the full hydrogenation of 2-phenyl-6-methyl-pyridine catalyzed by the Lewis acid C6F5(CH2)2B(C6F5)2 was investigated in detail by density functional theory calculations. Our calculations show that a plausible reaction pathway of the hydrogenation of pyridine contains five stages: (1) the generation of a new borane C6F5(CH2)2B(C6F5)2 from the hydroboration of the alkene, which forms a frustrated Lewis pair (FLP) with a pyridine; (2) the activation of H2 by FLP to yield an ion pair intermediate; (3) intramolecular hydride transfer from the boron atom to the pyridinium cation in the ion pair intermediate to produce the 1,4-dihydropyridine; (4) hydrogenation of the 1,4-dihydropyridine by the FLP to form the 1,4,5,6-tetrahydropyridine; (5) hydrogenation of the 1,4,5,6-tetrahydropyridine by the FLP to yield the final piperidine. The last two hydrogenation processes follow a similar pathway, which includes four steps: (a) proton transfer from the pyridinium moiety to the substrate; (b) dissociation of the newly generated pyridine; (c) hydride migration from the hydridoborate moiety to the protonated substrate to produce the hydrogenated product; (d) release of the hydrogenated product to regenerate the free borane. The full hydrogenation of pyridine is calculated to be exothermic by 16.9 kcal mol−1, relative to the starting reactants. The rate-limiting step is the proton transfer in the second hydrogenation step, with a free energy barrier of 28.2 kcal mol−1 in the gas phase (27.9 kcal mol−1 in toluene) at room temperature and 1.0 atm. Our results can account for the observed experimental facts.
Complexes containing a Ru2n+ core (n = 4, 5 or 6) have been of great interest because of their variety of electronic configurations and magnetic properties. Herein, we report a novel homovalent Ru26+-based complex, (H2pip)2[Ru2(hedp)2Cl2]·6H2O (pip = piperazine) (1), isolated by the direct reaction of the mixed-valent Ru25+-based anion Ru2(hedp)23− [hedp = 1-hydroxyethylidenediphosphonate, CH3C(OH)(PO3)2] with oxidant peracetic acid under room temperature conditions. Magnetic measurements unambiguously confirm that this complex contains four unpaired electrons with a spin ground state of S = 2.
Co-reporter:Dandan Yuan, Xiaoling Shen, Wei Li and Shuhua Li
Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 24) pp:NaN16500-16500
Publication Date(Web):2016/05/25
DOI:10.1039/C6CP01931E
Fragment-based quantum chemistry methods are either based on the many-body expansion or the inclusion–exclusion principle. To compare the applicability of these two categories of methods, we have systematically evaluated the performance of the generalized energy based fragmentation (GEBF) method (J. Phys. Chem. A, 2007, 111, 2193) and the electrostatically embedded many-body (EE-MB) method (J. Chem. Theory Comput., 2007, 3, 46) for medium-sized water clusters (H2O)n (n = 10, 20, 30). Our calculations demonstrate that the GEBF method provides uniformly accurate ground-state energies for 10 low-energy isomers of three water clusters under study at a series of theory levels, while the EE-MB method (with one water molecule as a fragment and without using the cutoff distance) shows a poor convergence for (H2O)20 and (H2O)30 when the basis set contains diffuse functions. Our analysis shows that the neglect of the basis set superposition error for each subsystem has little effect on the accuracy of the GEBF method, but leads to much less accurate results for the EE-MB method. The accuracy of the EE-MB method can be dramatically improved by using an appropriate cutoff distance and using two water molecules as a fragment. For (H2O)30, the average deviation of the EE-MB method truncated up to the three-body level calculated using this strategy (relative to the conventional energies) is about 0.003 hartree at the M06-2X/6-311++G** level, while the deviation of the GEBF method with a similar computational cost is less than 0.001 hartree. The GEBF method is demonstrated to be applicable for electronic structure calculations of water clusters at any basis set.
Physical Chemistry Chemical Physics 2012 - vol. 14(Issue 21) pp:NaN7862-7862
Publication Date(Web):2012/03/12
DOI:10.1039/C2CP23916G
A refined cluster-in-molecule (CIM) method for local correlation calculations of large molecules is presented. In the present work, two new strategies are introduced to further improve the CIM approach: (1) Some medium-range electron correlation energies, which are neglected in the previous CIM approach, are taken into account. (2) A much simpler procedure using only a distance threshold is used to construct various clusters. To cover the medium-range correlation effect as much as possible, some two-atom-centered clusters are built, in addition to one-atom-centered clusters. Our test calculations at the second order perturbation theory (MP2) level show that the refined CIM method can recover about 99.9% of the conventional MP2 correlation energy using an appropriate distance threshold. The accuracy of the present CIM method is capable of providing reliable relative energies of medium-sized systems such as polyalanines with 10 residues, and water molecules with 50 water molecules. For polyalanines with up to 30 residues, we have demonstrated that the computational cost of the CIM-MP2 calculation increases linearly with the molecular size, but the required memory and disc-space do not need to increase for large systems. The improved CIM method has been used to compute the relative energy of ice-like (H2O)96 clusters (with 2400 basis functions) and to predict the dimerization energy of a double-helical foldamer (with 2330 basis functions). The present CIM method is expected to be a practical local correlation method for describing the relative energies of large systems.
Co-reporter:Jun Shen, Enhua Xu, Zhuangfei Kou and Shuhua Li
Physical Chemistry Chemical Physics 2011 - vol. 13(Issue 19) pp:NaN8804-8804
Publication Date(Web):2011/03/29
DOI:10.1039/C0CP01103G
Here we review the basic formalism, implementation details, and performance of two newly developed coupled cluster (CC) methods based on the unrestricted Hartree–Fock (UHF) reference for treating molecules with multireference character. These two approaches can be considered to be approximations to the CC singles, doubles, and triples (CCSDT) method. The key concept of these two approaches is the corresponding orbitals, which are unitary transformations of canonical UHF molecular orbitals so that all spin orbitals are grouped into unique orbital pairs. In one approach called CCSDT(5P), a subset of triple excitations involving up to five-pair indices is included. In another approach called CCSD(T)-h, the contribution of connected triple excitations is treated in a hybrid way. With the concept of active corresponding orbitals, triple excitations can be automatically partitioned into two subsets, and the amplitudes of these two subsets are determined via solving different equations. Both CCSD(T)-h and CCSDT(5P) computationally scale as the seventh power of the system size. A survey of a number of applications demonstrates that CCSD(T)-h is an excellent approximation to the full CCSDT method, and CCSDT(5P) provides a good approximation to CCSDT for single-bond breaking processes. The overall performance of CCSDT(5P) is less accurate than that of CCSD(T)-h, but significantly better than that of the widely used CCSD(T).
![Phosphine, [4-[bis(2,3,4,5,6-pentafluorophenyl)boryl]-2,3,5,6-tetrafluorophenyl]bis(2,4,6-trimethylphenyl)-](/data/chemimg/3726100/918824-13-2.png)
![Phosphine, [4-[bis(2,3,4,5,6-pentafluorophenyl)boryl]-2,3,5,6-tetrafluorophenyl]bis(2,4,6-trimethylphenyl)-](/data/chemimg/3726100/918824-13-2_b.png)
![Ruthenium,[6-[[bis(1,1-dimethylethyl)phosphino-kP]methylene]-N,N-diethyl-1,6-dihydro-2-pyridinemethanaminato-kN1,kN2]carbonylhydro-, (SP-5-52)-](http://img.cochemist.com/ccimg/864000/863971-63-5.png)
![Ruthenium,[6-[[bis(1,1-dimethylethyl)phosphino-kP]methylene]-N,N-diethyl-1,6-dihydro-2-pyridinemethanaminato-kN1,kN2]carbonylhydro-, (SP-5-52)-](http://img.cochemist.com/ccimg/864000/863971-63-5_b.png)
![Phenol, 2-[(4-morpholinylimino)methyl]-](http://img.cochemist.com/ccimg/374700/374637-21-5.png)
![Phenol, 2-[(4-morpholinylimino)methyl]-](http://img.cochemist.com/ccimg/374700/374637-21-5_b.png)
![Heptanenitrile, 2-methyl-2-[(trimethylsilyl)oxy]-, (2R)-](http://img.cochemist.com/ccimg/291300/291273-67-1.png)
![Heptanenitrile, 2-methyl-2-[(trimethylsilyl)oxy]-, (2R)-](http://img.cochemist.com/ccimg/291300/291273-67-1_b.png)
![Pyrazolo[1,5,4-de]-1,4-benzoxazine, 6-(2-furanyl)-2,3-dihydro-](http://img.cochemist.com/ccimg/205000/204925-73-5.png)
![Pyrazolo[1,5,4-de]-1,4-benzoxazine, 6-(2-furanyl)-2,3-dihydro-](http://img.cochemist.com/ccimg/205000/204925-73-5_b.png)
![Methyl, [1,1':4',1''-terphenyl]-2,3',3''-triyltris-](http://img.cochemist.com/ccimg/193000/192933-25-8.png)
![Methyl, [1,1':4',1''-terphenyl]-2,3',3''-triyltris-](http://img.cochemist.com/ccimg/193000/192933-25-8_b.png)
![Methyl, tris[3-[bis[3-(1,1-dimethylethyl)phenyl]methylene]phenyl]-](http://img.cochemist.com/ccimg/193000/192933-23-6.png)
![Methyl, tris[3-[bis[3-(1,1-dimethylethyl)phenyl]methylene]phenyl]-](http://img.cochemist.com/ccimg/193000/192933-23-6_b.png)
![Tetracyclo[13.3.1.13,7.19,13]heneicosa-1(19),3,5,7(21),9,11,13(20),15,1
7-nonaene-2,8,14-triyl](http://img.cochemist.com/ccimg/193000/192933-21-4.png)
![Tetracyclo[13.3.1.13,7.19,13]heneicosa-1(19),3,5,7(21),9,11,13(20),15,1
7-nonaene-2,8,14-triyl](http://img.cochemist.com/ccimg/193000/192933-21-4_b.png)
![Methyl, [1,1':4',1''-terphenyl]-3,4''-diylbis-](http://img.cochemist.com/ccimg/193000/192933-13-4.png)
![Methyl, [1,1':4',1''-terphenyl]-3,4''-diylbis-](http://img.cochemist.com/ccimg/193000/192933-13-4_b.png)
![1,3-Benzenedicarboxylic acid, 5-[(4-carboxybenzoyl)amino]-](http://img.cochemist.com/ccimg/143400/143330-18-1.png)
![1,3-Benzenedicarboxylic acid, 5-[(4-carboxybenzoyl)amino]-](http://img.cochemist.com/ccimg/143400/143330-18-1_b.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1S,2S,4S)-](http://img.cochemist.com/ccimg/142600/142506-91-0.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1S,2S,4S)-](http://img.cochemist.com/ccimg/142600/142506-91-0_b.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1R,2R,4R)-](http://img.cochemist.com/ccimg/127000/126924-44-5.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1R,2R,4R)-](http://img.cochemist.com/ccimg/127000/126924-44-5_b.png)
![Heptanenitrile, 2-methyl-2-[(trimethylsilyl)oxy]-](http://img.cochemist.com/ccimg/111900/111874-59-0.png)
![Heptanenitrile, 2-methyl-2-[(trimethylsilyl)oxy]-](http://img.cochemist.com/ccimg/111900/111874-59-0_b.png)
![3-[(e)-2-butenoyl]-1,3-oxazolidin-2-one](http://img.cochemist.com/ccimg/109300/109299-92-5.png)
![3-[(e)-2-butenoyl]-1,3-oxazolidin-2-one](http://img.cochemist.com/ccimg/109300/109299-92-5_b.png)
![2H-Benzo[b][1,4]oxazin-4(3H)-amine](http://img.cochemist.com/ccimg/104300/104255-56-3.png)
![2H-Benzo[b][1,4]oxazin-4(3H)-amine](http://img.cochemist.com/ccimg/104300/104255-56-3_b.png)
![Diazene, bis[4-(trifluoromethyl)phenyl]-, (E)-](http://img.cochemist.com/ccimg/98300/98217-62-0.png)
![Diazene, bis[4-(trifluoromethyl)phenyl]-, (E)-](http://img.cochemist.com/ccimg/98300/98217-62-0_b.png)
![1(2H)-Quinolinamine, 3,4-dihydro-N-[(4-methoxyphenyl)methylene]-](http://img.cochemist.com/ccimg/87900/87866-72-6.png)
![1(2H)-Quinolinamine, 3,4-dihydro-N-[(4-methoxyphenyl)methylene]-](http://img.cochemist.com/ccimg/87900/87866-72-6_b.png)
![1,2-DIAZABICYCLO[3.1.0]HEX-2-ENE](http://img.cochemist.com/ccimg/81200/81194-34-5.png)
![1,2-DIAZABICYCLO[3.1.0]HEX-2-ENE](http://img.cochemist.com/ccimg/81200/81194-34-5_b.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1R,2S,4R)-](http://img.cochemist.com/ccimg/72300/72204-08-1.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1R,2S,4R)-](http://img.cochemist.com/ccimg/72300/72204-08-1_b.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1S,2R,4S)-](http://img.cochemist.com/ccimg/72300/72203-36-2.png)
![Bicyclo[2.2.1]hept-5-ene-2-carboxaldehyde, 2-methyl-, (1S,2R,4S)-](http://img.cochemist.com/ccimg/72300/72203-36-2_b.png)
![2,3-DIAZABICYCLO[2.1.1]HEX-2-ENE](http://img.cochemist.com/ccimg/72200/72192-13-3.png)
![2,3-DIAZABICYCLO[2.1.1]HEX-2-ENE](http://img.cochemist.com/ccimg/72200/72192-13-3_b.png)
![Benzo[3,4]cyclobuta[1,2-a]biphenylene](/data/chemimg/2538300/65513-20-4.png)
![Benzo[3,4]cyclobuta[1,2-a]biphenylene](/data/chemimg/2538300/65513-20-4_b.png)
![Tricyclo[6.2.0.02,5]deca-1,3,5,7,9-pentaene](/data/chemimg/2719700/61960-82-5.png)
![Tricyclo[6.2.0.02,5]deca-1,3,5,7,9-pentaene](/data/chemimg/2719700/61960-82-5_b.png)
![BENZENESULFONIC ACID, [(4-METHYLPHENYL)METHYLENE]HYDRAZIDE](http://img.cochemist.com/ccimg/50700/50626-25-0.png)
![BENZENESULFONIC ACID, [(4-METHYLPHENYL)METHYLENE]HYDRAZIDE](http://img.cochemist.com/ccimg/50700/50626-25-0_b.png)
![Thiazolium, 3-[(4-amino-2-methyl-5-pyrimidinyl)methyl]-2-(1-carboxy-1-hydroxyethyl)-4-methyl-5-(4,6,6-trihydroxy-4,6-dioxido-3,5-dioxa-4,6-](/data/chemimg/1182300/29560-79-0.png)
![Thiazolium, 3-[(4-amino-2-methyl-5-pyrimidinyl)methyl]-2-(1-carboxy-1-hydroxyethyl)-4-methyl-5-(4,6,6-trihydroxy-4,6-dioxido-3,5-dioxa-4,6-](/data/chemimg/1182300/29560-79-0_b.png)
![Benzo[3,4]cyclobuta[1,2-b]biphenylene](http://img.cochemist.com/ccimg/24800/24756-50-1.png)
![Benzo[3,4]cyclobuta[1,2-b]biphenylene](http://img.cochemist.com/ccimg/24800/24756-50-1_b.png)
![Tricyclo[6.2.0.03,6]deca-1,3,5,7,9-pentaene](http://img.cochemist.com/ccimg/24500/24447-42-5.png)
![Tricyclo[6.2.0.03,6]deca-1,3,5,7,9-pentaene](http://img.cochemist.com/ccimg/24500/24447-42-5_b.png)
![Bis[(pentamethylcyclopentadienyl)dichloro-rhodium]](http://img.cochemist.com/ccimg/12400/12354-85-7.png)
![Bis[(pentamethylcyclopentadienyl)dichloro-rhodium]](http://img.cochemist.com/ccimg/12400/12354-85-7_b.png)
![Cycloprop[a]inden-6(1H)-one, 1a,6a-dihydro-](http://img.cochemist.com/ccimg/5800/5771-62-0.png)
![Cycloprop[a]inden-6(1H)-one, 1a,6a-dihydro-](http://img.cochemist.com/ccimg/5800/5771-62-0_b.png)
![Cyclobut[a]anthracene](http://img.cochemist.com/ccimg/4100/4026-25-9.png)
![Cyclobut[a]anthracene](http://img.cochemist.com/ccimg/4100/4026-25-9_b.png)
![Bicyclo[4.2.0]octa-1,3,5,7-tetraene](/data/chemimg/58400/4026-23-7.png)
![Bicyclo[4.2.0]octa-1,3,5,7-tetraene](/data/chemimg/58400/4026-23-7_b.png)
![2,3-DIAZABICYCLO[2.2.2]OCT-2-ENE](http://img.cochemist.com/ccimg/3400/3310-62-1.png)
![2,3-DIAZABICYCLO[2.2.2]OCT-2-ENE](http://img.cochemist.com/ccimg/3400/3310-62-1_b.png)
![Hydrazine, 1,2-bis[4-(trifluoromethyl)phenyl]-](http://img.cochemist.com/ccimg/800/740-69-2.png)
![Hydrazine, 1,2-bis[4-(trifluoromethyl)phenyl]-](http://img.cochemist.com/ccimg/800/740-69-2_b.png)
![Cyclobuta[b]naphthalene](/data/chemimg/493800/277-98-5.png)
![Cyclobuta[b]naphthalene](/data/chemimg/493800/277-98-5_b.png)
![Cyclobut[b]anthracene](http://img.cochemist.com/ccimg/300/259-58-5.png)
![Cyclobut[b]anthracene](http://img.cochemist.com/ccimg/300/259-58-5_b.png)
![Dibenzo[b,h]biphenylene](http://img.cochemist.com/ccimg/300/258-47-9.png)
![Dibenzo[b,h]biphenylene](http://img.cochemist.com/ccimg/300/258-47-9_b.png)
![Benzo[a]biphenylene(6CI,7CI,8CI,9CI)](http://img.cochemist.com/ccimg/300/252-47-1.png)
![Benzo[a]biphenylene(6CI,7CI,8CI,9CI)](http://img.cochemist.com/ccimg/300/252-47-1_b.png)
![Dibenzo[a,i]biphenylene](http://img.cochemist.com/ccimg/300/252-24-4.png)
![Dibenzo[a,i]biphenylene](http://img.cochemist.com/ccimg/300/252-24-4_b.png)
![Cyclobuta[a]naphthalene](/data/chemimg/436400/249-99-0.png)
![Cyclobuta[a]naphthalene](/data/chemimg/436400/249-99-0_b.png)
![Benzo[a]naphthacene](http://img.cochemist.com/ccimg/300/226-88-0.png)
![Benzo[a]naphthacene](http://img.cochemist.com/ccimg/300/226-88-0_b.png)
![Dibenz[a,j]anthracene](http://img.cochemist.com/ccimg/300/224-41-9.png)
![Dibenz[a,j]anthracene](http://img.cochemist.com/ccimg/300/224-41-9_b.png)
![Benzo[g]chrysene](http://img.cochemist.com/ccimg/200/196-78-1.png)
![Benzo[g]chrysene](http://img.cochemist.com/ccimg/200/196-78-1_b.png)
![Naphth[1,2-a]anthracene](http://img.cochemist.com/ccimg/200/195-06-2.png)
![Naphth[1,2-a]anthracene](http://img.cochemist.com/ccimg/200/195-06-2_b.png)
![Benzo[c]chrysene](http://img.cochemist.com/ccimg/200/194-69-4.png)
![Benzo[c]chrysene](http://img.cochemist.com/ccimg/200/194-69-4_b.png)
![Dinaphtho[2,1-d:1',2'-f][1,3]dioxepin](http://img.cochemist.com/ccimg/200/188-35-2.png)
![Dinaphtho[2,1-d:1',2'-f][1,3]dioxepin](http://img.cochemist.com/ccimg/200/188-35-2_b.png)
![bicyclo[2.2.0]hexane](http://img.cochemist.com/ccimg/200/186-04-9.png)
![bicyclo[2.2.0]hexane](http://img.cochemist.com/ccimg/200/186-04-9_b.png)
![Bicyclo[1.1.0]butane](http://img.cochemist.com/ccimg/200/157-33-5.png)
![Bicyclo[1.1.0]butane](http://img.cochemist.com/ccimg/200/157-33-5_b.png)
